The costs should be identical. The only difference is the instant gratification of walking out with your purchase right then and there..........
Even most of the upgrade deals that are touted on the online store can be had at the "brick and mortar", if you just ask.
I was able to get the RAM upgrade, and the $30 off for iWork, and have the pleasure of enjoying my purchase as soon as I got home, instead of waiting a week or so........